访问Ensembl ID
查找智人(homo sapien)基因组
https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/accessing_ensembl.html#introduction
Code
# BiocManager::install("biomaRt")
library(biomaRt)
listEnsembl()
#> biomart version
#> 1 genes Ensembl Genes 115
#> 2 mouse_strains Mouse strains 115
#> 3 snps Ensembl Variation 115
#> 4 regulation Ensembl Regulation 115
# 连接ENSEMBL数据库 智人基因数据集
ensembl <- useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl")
ensembl
#> Object of class 'Mart':
#> Using the ENSEMBL_MART_ENSEMBL BioMart database
#> Using the hsapiens_gene_ensembl dataset
# 获取基因信息
genes <- getBM(attributes = c("ensembl_gene_id", "hgnc_symbol", "chromosome_name",
"start_position", "end_position", "gene_biotype"),
mart = ensembl)
genes |> DT::datatable()
Code
# 获取转录本信息
transcripts <- getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id",
"transcript_start", "transcript_end"),
mart = ensembl)
transcripts |> DT::datatable()